The excellent fanficNeon Genesis Evangelion: R proposes that the Second Branch, and EVA-04, were not destroyed by the Dirac sea, but instead merely 'sequestered' within it as EVA-01 was when eaten by Leliel, the 12th Angel.

The Evangelion itself is never seen in the series proper (i.e., the 26 TV episodes), though a brief glimpse of it appears in Evangelion: Death. It is either silver or white in color (the art in that brief shot is ambiguous, but the models of it available are all silver vice white). Other than its color, it is outwardly identical to the pre-transformation EVA-03. This EVA never had a designated pilot. Who the pilot would have been, had the unit not been consumed, is a matter of some debate in the Evangelion fan community. The most likely candidates are Kensuke Aida, who begged to pilot EVA-03, and Hikari Horaki, who is the only other named classmate. It was, however, stated in the series that all of Shinji's classmates were pilot candidates.